RegulonDB RegulonDB 10.8: Gene Form
   

adk gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

hemH adk nc2 aes OxyR OxyR terminator hemHp hemHp adkp adkp TSS_641 TSS_641

Gene      
Name: adk    Texpresso search in the literature
Synonym(s): ECK0468, EG10032, b0474, dnaW, plsA
Genome position(nucleotides): 497175 --> 497819 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
51.78
External database links:  
ASAP:
ABE-0001645
CGSC:
1040
ECHOBASE:
EB0031
MIM:
267500
OU-MICROARRAY:
b0474
PortEco:
adk
STRING:
511145.b0474
COLOMBOS: adk


Product      
Name: adenylate kinase
Synonym(s): Adk, DnaW, PlsA
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 23.586
Isoelectric point: 5.448
Motif(s):
 
Type Positions Sequence
123 -> 158 RRVHAPSGRVYHVKFNPPKVEGKDDVTGEELTTRKD
132 -> 133 VY
13 -> 13 K
30 -> 59 STGDMLRAAVKSGSELGKQAKDIMDAGKLV
9 -> 9 P

 

Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.5 - biosynthesis of building blocks --> 1.5.2 - nucleotides --> 1.5.2.3 - purine ribonucleotide biosynthesis
  1 - metabolism --> 1.7 - central intermediary metabolism --> 1.7.33 - nucleotide and nucleoside conversions
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
GO:0005829 - cytosol
molecular_function GO:0005515 - protein binding
GO:0016740 - transferase activity
GO:0016301 - kinase activity
GO:0016776 - phosphotransferase activity, phosphate group as acceptor
GO:0000166 - nucleotide binding
GO:0005524 - ATP binding
GO:0004017 - adenylate kinase activity
GO:0004550 - nucleoside diphosphate kinase activity
GO:0019205 - nucleobase-containing compound kinase activity
GO:0000287 - magnesium ion binding
GO:0016208 - AMP binding
biological_process GO:0046940 - nucleoside monophosphate phosphorylation
GO:0006139 - nucleobase-containing compound metabolic process
GO:0009165 - nucleotide biosynthetic process
GO:0016310 - phosphorylation
GO:0015951 - purine ribonucleotide interconversion
GO:0006165 - nucleoside diphosphate phosphorylation
GO:0006172 - ADP biosynthetic process
GO:0044209 - AMP salvage
Note(s): Note(s): ...[more].
Reference(s): [1] Billerbeck S., et al., 2012
[2] Chen B., et al., 2009
[3] Joseph AP., et al., 2016
[4] Lee HJ., et al., 2011
[5] Lerner E., et al., 2013
[6] Liu X., et al., 2015
[7] Luo D., et al., 2016
[8] Mahmud R., et al., 2019
[9] Matsunaga Y., et al., 2012
[10] Morishita T., et al., 2017
[11] Oesterle S., et al., 2017
[12] Ponzoni L., et al., 2015
[13] Sun Y., et al., 2011
[14] Yuan W., et al., 2008
External database links:  
DIP:
DIP-47903N
ECOCYC:
ADENYL-KIN-MONOMER
ECOLIWIKI:
b0474
INTERPRO:
IPR006259
INTERPRO:
IPR033690
INTERPRO:
IPR027417
INTERPRO:
IPR007862
INTERPRO:
IPR000850
MODBASE:
P69441
PANTHER:
PTHR23359
PDB:
4X8O
PDB:
5EJE
PDB:
6F7U
PDB:
6HAM
PDB:
4X8L
PDB:
4X8H
PDB:
4AKE
PDB:
3HPR
PDB:
3HPQ
PDB:
2ECK
PDB:
1E4Y
PDB:
1E4V
PDB:
1ANK
PDB:
1AKE
PDB:
4X8M
PFAM:
PF05191
PRIDE:
P69441
PRINTS:
PR00094
PRODB:
PRO_000022061
PROSITE:
PS00113
REFSEQ:
NP_415007
SMR:
P69441
UNIPROT:
P69441


Operon      
Name: adk         
Operon arrangement:
Transcription unit        Promoter
adk


RNA cis-regulatory element    
Attenuation: Transcriptional


Elements in the selected gene context region unrelated to any object in RegulonDB      

  Type Name Post Left Post Right Strand Notes Evidence (Confirmed, Strong, Weak) References
  promoter TSS_641 497133 forward nd [RS-EPT-CBR] [15]


Evidence    

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates



Reference(s)    

 [1] Billerbeck S., Panke S., 2012, A genetic replacement system for selection-based engineering of essential proteins., Microb Cell Fact 11:110

 [2] Chen B., Sysoeva TA., Chowdhury S., Guo L., Nixon BT., 2009, ADPase activity of recombinantly expressed thermotolerant ATPases may be caused by copurification of adenylate kinase of Escherichia coli., FEBS J 276(3):807-15

 [3] Joseph AP., Malhotra S., Burnley T., Wood C., Clare DK., Winn M., Topf M., 2016, Refinement of atomic models in high resolution EM reconstructions using Flex-EM and local assessment., Methods 100:42-9

 [4] Lee HJ., Ho MR., Tseng CS., Hsu CY., Huang MS., Peng HL., Chang HY., 2011, Exponential ATP amplification through simultaneous regeneration from AMP and pyrophosphate for luminescence detection of bacteria., Anal Biochem 418(1):19-23

 [5] Lerner E., Hilzenrat G., Amir D., Tauber E., Garini Y., Haas E., 2013, Preparation of homogeneous samples of double-labelled protein suitable for single-molecule FRET measurements., Anal Bioanal Chem 405(18):5983-91

 [6] Liu X., Huang A., Luo D., Liu H., Han H., Xu Y., Liang P., 2015, Use of adenylate kinase as a solubility tag for high level expression of T4 DNA ligase in Escherichia coli., Protein Expr Purif 109:79-84

 [7] Luo D., Wen C., Zhao R., Liu X., Cui J., Liang JG., Liang P., 2016, High Level Expression and Purification of Recombinant Proteins from Escherichia coli with AK-TAG., PLoS One 11(5):e0156106

 [8] Mahmud R., Shehreen S., Shahriar S., Rahman MS., Akhteruzzaman S., Sajib AA., 2019, Non-Caloric Artificial Sweeteners Modulate the Expression of Key Metabolic Genes in the Omnipresent Gut Microbe Escherichia coli., J Mol Microbiol Biotechnol :1-14

 [9] Matsunaga Y., Fujisaki H., Terada T., Furuta T., Moritsugu K., Kidera A., 2012, Minimum free energy path of ligand-induced transition in adenylate kinase., PLoS Comput Biol 8(6):e1002555

 [10] Morishita T., Yonezawa Y., Ito AM., 2017, Free Energy Reconstruction from Logarithmic Mean-Force Dynamics Using Multiple Nonequilibrium Trajectories., J Chem Theory Comput 13(7):3106-3119

 [11] Oesterle S., Roberts TM., Widmer LA., Mustafa H., Panke S., Billerbeck S., 2017, Sequence-based prediction of permissive stretches for internal protein tagging and knockdown., BMC Biol 15(1):100

 [12] Ponzoni L., Polles G., Carnevale V., Micheletti C., 2015, SPECTRUS: A Dimensionality Reduction Approach for Identifying Dynamical Domains in Protein Complexes from Limited Structural Datasets., Structure 23(8):1516-1525

 [13] Sun Y., Fukamachi T., Saito H., Kobayashi H., 2011, ATP requirement for acidic resistance in Escherichia coli., J Bacteriol 193(12):3072-7

 [14] Yuan W., Yang J., Kopeckova P., Kopecek J., 2008, Smart hydrogels containing adenylate kinase: translating substrate recognition into macroscopic motion., J Am Chem Soc 130(47):15760-1

 [15] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.


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